How does this affect my backup?

If you plug your external hard drive in to your computer, it is
likely that Spotlight will begin to index the files on this
drive... a very bad idea if this is your backup drive! With
an indexed backup drive, multiple instances of the file you wish to
open may appear in your search results. With the location of the
file not shown in the search results, it's easy to
mistakenly open the file on your backup, instead of on your hard
drive.

Imagine opening a file with Spotlight, working for 3 hours,
saving the document, and then running your backup... if you opened
up the file from your backup, then *poof* it's gone,
replaced by the unchanged copy you have on your computer's
hard drive.